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2012: Gen. Allen caught in Petraeus scandal

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He was the top coalition commander in Afghanistan for nearly two years

Allen was nominated to be the supreme allied commander of NATO

He was cleared of any wrongdoing in a scandal over embarrassing e-mails

Gen. John Allen, the former leader of coalition forces in Afghanistan who was nominated to become supreme allied commander of NATO, is retiring instead of continuing to pursue the post, President Barack Obama announced Tuesday.

Allen informed Obama that he will leave the service rather than move forward with the nomination, which requires Senate confirmation, a White House statement said.

"I met with General John Allen and accepted his request to retire from the military so that he can address health issues within his family," Obama said.

In a statement later Tuesday, Allen said his reasons for retiring were personal.

"While I won't go into the details, my primary concern is for the health of my wife, who has sacrificed so much for so long. For more than 35 years, my beloved Kathy has devotedly stood beside me and enabled me to serve my country.

"It is profoundly sobering to consider how much of that time I have spent away from her and our two precious daughters. It is now my turn to stand beside them, to be there for them when they need me most," he said.

Who is calling the shots in Afghanistan?

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Kelley's connection to General Allen

Allen, a Marine Corps general, was the top coalition commander in Afghanistan for nearly two years. He relinquished that command earlier this month after planning the end of the mission's combat operations.

CNN previously reported that Defense Department officials said there was inappropriate language in those e-mails, but no evidence of an affair between Allen and Kelley.

Allen's nomination for the NATO commander post was put on hold while the Pentagon's inspector general looked into the issue.

He was cleared of wrongdoing after several months and the White House initially indicated Obama would proceed with the nomination.

On Tuesday, Obama called the general one of America's finest military leaders.

Allen "presided over the significant growth in the size and capability of Afghan National Security Forces, the further degradation of al Qaeda and their extremist allies, and the ongoing transition to Afghan security responsibility across the country," Obama said in the statement.

Defense Secretary Leon Panetta said in a statement on Tuesday that Allen's leadership in Afghanistan "will be long remembered as pivotal" to the mission.

"The strategy he developed and implemented has put us on the right path towards completing this mission, with Afghan forces now on track to step into the lead for security nationwide this spring and to assume full security responsibility by the end of next year," Panetta said.

Panetta, who also is stepping down, previously acknowledged that Allen has "been under a tremendous amount of pressure," and advised him to take his time in deciding whether to continue pursuing the NATO commander position.

In July 2011, Allen succeeded Petraeus to inherit the largest-ever NATO force in Afghanistan and spent 19 months directing his forces against Taliban insurgents and preparing for the first phases of a hand-over of provincial security to local and national forces.

About 150,000 ISAF members were deployed at that time, including just under 100,000 U.S. troops. There are 66,000 U.S. service members currently deployed to the region, and Obama announced last week his intention to bring home 34,000 of them within a year.

Less than a month after he assumed command, the United States suffered its deadliest single attack of the Afghan war when insurgents downed a CH-47 Chinook helicopter in Wardak province, killing 30 U.S. service members. The toll included 22 Navy SEALs.

Allen later faced additional diplomatic crises that followed controversial incidents that included the accidental burning of Qurans by U.S. service members, U.S. airstrikes that resulted in civilian deaths and the killing of 16 civilians in a massacre allegedly carried out by a U.S. service member.

An uptick in "green-on-blue" attacks -- in which Afghan forces or trainees turn their weapons against U.S. counterparts -- is also believed to have hampered the training of Afghan forces and contributed to increased public discontent at home over American deployment to the region.

A graduate of Georgetown University and the National War College, Allen also drew distinction for his counterinsurgency work in Iraq, particularly in the country's volatile Anbar province in 2008, where he helped isolate a growing insurgency.